This study uses nanopore sequencing technology to analyze the gut bacterial flora composition of Taiwanese cultured clams. Through the analysis of the Epi2me platform, among the 12 gut microbiota samples of the cultured clams from Cigu, Tainan, a total of 415,881 valid 16S sequences were successfully sequenced, and 314,348 of these sequences can be identified to the genus level. The 5 bacteria genera with the highest proportion in clam gut bacterial flora are Vibrio, Mycoplasma, Endozoicomonas, Bacillus, Anoxybacillus. The nanopore sequencing reported greater taxonomic resolution than other sequencing platforms and its slightly lower per read accuracy did not seem to affect the analysis very much. Both software and hardware of nanopore sequencing technology is under continuous development, and its sequencing accuracy is also continuously increasing, which has great potential for gut bacterial flora analysis.